Contacts of the strand formed by residues 220 - 224 (chain A) in PDB entry 5C51
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.4 21.8 - - + +
163A PRO* 2.7 40.9 + - + -
164A PRO 4.2 5.6 + - - -
165A LYS* 3.5 31.6 - - + -
166A PRO* 4.5 7.6 - - + -
169A TRP* 3.9 17.9 - + - -
177A ARG* 3.5 2.8 - - - -
178A TYR* 2.9 45.5 + - + +
213A VAL* 3.8 13.5 - - + -
214A ALA 4.0 2.5 - - - -
215A ILE* 3.5 35.0 - - + +
219A ALA* 1.3 77.0 - - - +
221A TYR* 1.3 75.5 - - - +
397A ALA* 3.7 33.4 - - + -
400A VAL* 4.5 0.2 - - + -
401A TRP* 4.8 9.2 - + + -
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Residues in contact with TYR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A TRP* 5.4 0.4 - - - -
175A TRP* 3.6 23.6 - + + -
176A THR 3.2 8.1 - - - -
177A ARG* 2.7 55.1 + - + -
178A TYR* 4.3 2.5 - - - -
187A VAL* 5.0 5.8 - - + -
190A PRO* 3.7 33.1 - - + +
191A GLU 4.5 4.2 + - - -
192A GLU* 3.1 27.2 + - + +
195A LEU* 5.1 4.0 - - + -
213A VAL* 3.5 7.8 - - - +
214A ALA* 2.9 43.3 + - + +
216A SER* 3.5 26.0 - - - -
219A ALA 4.2 0.7 - - - -
220A TRP* 1.3 88.4 - - - +
222A SER* 1.3 59.7 + - - +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 3.8 17.7 - - - -
170A ALA 4.6 4.3 + - - -
172A ALA 5.5 0.3 - - - +
174A GLY 3.6 2.4 - - - +
175A TRP* 3.9 1.3 - - - -
176A THR* 2.3 62.6 + - - +
178A TYR* 2.7 22.9 + - - -
212A ALA 3.5 8.7 - - - -
213A VAL* 4.6 0.4 - - - -
221A TYR* 1.3 75.0 - - - +
223A TRP* 1.3 61.1 + - - +
224A CYS* 4.0 0.9 + - - -
393A MET* 4.1 13.3 - - - +
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Residues in contact with TRP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY* 3.2 36.0 - - - -
175A TRP* 3.4 44.2 - + + -
199A VAL* 5.5 1.8 - - + -
209A PRO* 3.7 22.0 - - + -
211A LEU* 3.6 7.6 - - - -
212A ALA* 2.9 61.2 + - + +
222A SER* 1.3 71.9 - - - +
224A CYS* 1.3 70.4 + - - +
225A SER* 3.1 33.9 - - - -
240A SER 4.0 13.7 - - - -
242A ALA* 3.6 42.8 - - + -
243A ASP* 3.9 9.9 + - - -
279A ARG* 5.6 3.0 - - - +
393A MET* 3.9 3.3 - - - +
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Residues in contact with CYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ALA 4.3 5.8 - - - -
171A TRP* 4.9 0.9 - - - -
172A ALA 3.2 23.8 - - - +
173A GLU* 4.1 0.7 - - - +
174A GLY 2.9 28.5 + - - -
210A THR 3.9 1.8 - - - -
211A LEU* 3.6 13.2 - - - -
222A SER* 4.0 1.5 + - - -
223A TRP* 1.3 84.0 + - - +
225A SER* 1.3 63.1 + - - +
228A LEU* 4.0 21.3 - - + -
389A PHE* 3.6 34.5 - - - -
393A MET* 3.8 8.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il